SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics.
basic_science · Level V
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- Record sourced from PubMed, PMID 41413345.
- Also identified by DOI 10.1038/s41592-025-02968-w.
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Abstract
Imaging-based spatial transcriptomics methods allow for the measurement of spatial determinants of cellular phenotypes but are incompatible with random barcode-based clone-tracing methods, preventing the simultaneous detection of clonal and spatial drivers. Here we report SpaceBar, which enables simultaneous clone tracing and spatial gene expression profiling with standard imaging-based spatial transcriptomics pipelines. Our approach uses a library of 96 synthetic barcode sequences that combinatorially labels each cell. Thus, SpaceBar can distinguish between clonal dynamics and environmentally driven transcriptional regulation in complex tissue contexts.
Medical subject headings
- Single-Cell Analysis
- Gene Expression Profiling
- Transcriptome